Shortly after its opening the school became affiliated with Northern Baptist Theological Seminary in Chicago, Illinois.

This affiliation lasted until 1960, when the school became an accredited member of the Association for Theological Education in South East Asia.

In 1977, on Maung’s retirement, Thramu Esther Lwin was made acting-president and then president from June 1978 to the end of 1983.

Thramu Eh Wah, the vice-president, was made acting-president until March 1988, when she was officially appointed President.

Simon Pau Khan En succeeded in 2006, and when he retired in 2010, Samuel Ngun Ling became President of MIT (April 2010 - March 2023).

In 2004, MIT launched the Doctor of Ministry (DMin) program in partnership with the Union Theological Seminary, Manila, the Philippines.

In 2014, MIT launched the PhD degree program in the commemoration of the 200th anniversary of the arrival of the American Baptist missionaries, Adoniram and Ann Judson in the soil of Myanmar.